One map at a time.

I am making a wad that will have more than one map. https://sites.google.com/site/bldmcoop And I've been making the maps as separate map01 wads with plans to merge them in the future in whatever order I choose. The problem I'm seeing is in the patches and floors that I add. I'm using some of the same ones in different maps! Is that going to be an issue?

Don't know for sure, but why don't you create a separate texture wad (you can use textures and flats from a separate file in Doom Builder), remove all textures from the maps and then eventually just merge everything together?

Yea, you don't have to merge the WADs just yet if you don't want to. Just add the WAD file with the textures as a resource in Doom Builder and it will give you access to the textures. Later, when you're done with the whole thing, you should merge the WADs together before uploading it so that people don't have to start Doom with several files together (you can bet your money people won't do that if they don't read your text file... and people generally don't read).